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- PDB-9lyg: Crystal structure of FKBP12 complexed with Small Molecule Anchor ... -

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Basic information

Entry
Database: PDB / ID: 9lyg
TitleCrystal structure of FKBP12 complexed with Small Molecule Anchor for Protein-201
ComponentsPeptidyl-prolyl cis-trans isomerase FKBP1A
KeywordsISOMERASE / FK506-binding protein / FKBP12 / complex / binding protein / PPIase / peptidyl-prolyl cis-trans isomerase
Function / homology
Function and homology information


macrolide binding / activin receptor binding / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / cytoplasmic side of membrane / transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / type I transforming growth factor beta receptor binding / negative regulation of activin receptor signaling pathway / heart trabecula formation / I-SMAD binding ...macrolide binding / activin receptor binding / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / cytoplasmic side of membrane / transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / type I transforming growth factor beta receptor binding / negative regulation of activin receptor signaling pathway / heart trabecula formation / I-SMAD binding / signaling receptor inhibitor activity / regulation of amyloid precursor protein catabolic process / terminal cisterna / ryanodine receptor complex / 'de novo' protein folding / ventricular cardiac muscle tissue morphogenesis / FK506 binding / TGF-beta receptor signaling activates SMADs / mTORC1-mediated signalling / Calcineurin activates NFAT / regulation of ryanodine-sensitive calcium-release channel activity / regulation of immune response / heart morphogenesis / supramolecular fiber organization / sarcoplasmic reticulum membrane / calcium channel regulator activity / protein maturation / T cell activation / peptidyl-prolyl cis-trans isomerase activity / sarcoplasmic reticulum / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase / negative regulation of transforming growth factor beta receptor signaling pathway / Z disc / SARS-CoV-1 activates/modulates innate immune responses / protein folding / regulation of protein localization / protein refolding / amyloid fibril formation / Potential therapeutics for SARS / transmembrane transporter binding / positive regulation of canonical NF-kappaB signal transduction / membrane / cytosol / cytoplasm
Similarity search - Function
: / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / Peptidyl-prolyl cis-trans isomerase domain superfamily
Similarity search - Domain/homology
: / Peptidyl-prolyl cis-trans isomerase FKBP1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å
AuthorsKato, S. / Tsuchikawa, H. / Katoh, A. / Matsuoka, S. / Sugiyama, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)23ak0101198h0001 Japan
CitationJournal: To Be Published
Title: Crystal structure of FKBP12 complexed with Small Molecule Anchor for Protein-201
Authors: Kato, S. / Tsuchikawa, H. / Katoh, A. / Matsuoka, S. / Sugiyama, S.
History
DepositionFeb 20, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase FKBP1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9124
Polymers12,2501
Non-polymers6623
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area410 Å2
ΔGint-1 kcal/mol
Surface area6060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.577, 48.039, 65.306
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase FKBP1A / PPIase FKBP1A / 12 kDa FK506-binding protein / 12 kDa FKBP / FKBP-12 / Calstabin-1 / FK506-binding ...PPIase FKBP1A / 12 kDa FK506-binding protein / 12 kDa FKBP / FKBP-12 / Calstabin-1 / FK506-binding protein 1A / FKBP-1A / Immunophilin FKBP12 / Rotamase


Mass: 12249.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP1A, FKBP1, FKBP12 / Production host: Escherichia coli (E. coli) / References: UniProt: P62942, peptidylprolyl isomerase
#2: Chemical ChemComp-A1L7S / 5-[(2~{S})-1-cyclohexylsulfonylpiperidin-2-yl]-3-[3-(3,4-dimethoxyphenyl)propyl]-1,2,4-oxadiazole


Mass: 477.617 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H35N3O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M Tris-HCl (pH8.0), 3.0 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 6, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.26→38.7 Å / Num. obs: 27488 / % possible obs: 99.6 % / Redundancy: 17.5 % / Rpim(I) all: 0.161 / Net I/σ(I): 8.4
Reflection shellResolution: 1.26→1.28 Å / Num. unique obs: 1375 / CC1/2: 0.643

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PPN

2ppn


Resolution: 1.26→38.7 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.675 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18808 1324 4.8 %RANDOM
Rwork0.14698 ---
obs0.14889 26041 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.591 Å2
Baniso -1Baniso -2Baniso -3
1--0.87 Å2-0 Å2-0 Å2
2---0.56 Å20 Å2
3---1.43 Å2
Refinement stepCycle: 1 / Resolution: 1.26→38.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms832 0 45 120 997
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131070
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171006
X-RAY DIFFRACTIONr_angle_refined_deg1.9131.711465
X-RAY DIFFRACTIONr_angle_other_deg1.4271.6432370
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7455140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.37322.15751
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.85715183
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.071157
X-RAY DIFFRACTIONr_chiral_restr0.2240.2128
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021244
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02216
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3410.917518
X-RAY DIFFRACTIONr_mcbond_other1.3180.913517
X-RAY DIFFRACTIONr_mcangle_it1.9091.386672
X-RAY DIFFRACTIONr_mcangle_other1.9121.389673
X-RAY DIFFRACTIONr_scbond_it2.0991.177552
X-RAY DIFFRACTIONr_scbond_other2.0971.178553
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7151.655794
X-RAY DIFFRACTIONr_long_range_B_refined3.85712.6321184
X-RAY DIFFRACTIONr_long_range_B_other3.45111.8571149
X-RAY DIFFRACTIONr_rigid_bond_restr2.76932076
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.26→1.293 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 113 -
Rwork0.208 1835 -
obs--98.38 %

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